Usage

  • This R Markdown file imports data tables within Analysis_Results-Date folder and will knit without any modification.
  • ggsave code is kept for users to make customized plots.


Strain Issues

All strain names were converted to the corresponding isotype name, which can be looked up here: https://elegansvariation.org/strains/isotype_list. If you submitted replicate data, replicates for a given isotype were averaged to one mean value.

## [1] "No strain issues to report"

Manhattan plot

  • Every dot is a SNV marker.

  • SNVs are colored red if they pass the genome-wide corrected significance threshold:

    • The horizontal solid line corresponds to Bonferroni (BF) threshold
    • The horizontal dash line corresponds to EIGEN threshold (see below), which corrects for the number of independent markers in your data set.



Phenotype by Genotype Split

Linkage disequilibrium (LD) between QTL



Divergent region, haplotype, and fine mapping for each significant QTL region

Only for regions less than 5 Mb in size

I:2190874-3060001

Fine mapping

Fine mapping was performed by evaluating the genotype-phenotype relationship for variants nearby the QTL identified from GWA mapping using a vcf containing imputed variants to avoid removing variants with missing genotype information for one or a few strains. Only SNVs were considered in this mapping.



All variants in interval



Divergent regions



Haplotype




II:2419-1469463

Fine mapping

Fine mapping was performed by evaluating the genotype-phenotype relationship for variants nearby the QTL identified from GWA mapping using a vcf containing imputed variants to avoid removing variants with missing genotype information for one or a few strains. Only SNVs were considered in this mapping.



All variants in interval



Divergent regions



Haplotype




II:12906422-14197294

Fine mapping

Fine mapping was performed by evaluating the genotype-phenotype relationship for variants nearby the QTL identified from GWA mapping using a vcf containing imputed variants to avoid removing variants with missing genotype information for one or a few strains. Only SNVs were considered in this mapping.



All variants in interval



Divergent regions



Haplotype




III:2840634-3826415

Fine mapping

Fine mapping was performed by evaluating the genotype-phenotype relationship for variants nearby the QTL identified from GWA mapping using a vcf containing imputed variants to avoid removing variants with missing genotype information for one or a few strains. Only SNVs were considered in this mapping.



All variants in interval



Divergent regions



Haplotype




III:12050787-13208614

Fine mapping

Fine mapping was performed by evaluating the genotype-phenotype relationship for variants nearby the QTL identified from GWA mapping using a vcf containing imputed variants to avoid removing variants with missing genotype information for one or a few strains. Only SNVs were considered in this mapping.



All variants in interval



Divergent regions



Haplotype




X:1447600-3820231

Fine mapping

Fine mapping was performed by evaluating the genotype-phenotype relationship for variants nearby the QTL identified from GWA mapping using a vcf containing imputed variants to avoid removing variants with missing genotype information for one or a few strains. Only SNVs were considered in this mapping.



All variants in interval



Divergent regions



Haplotype




X:13688273-15231608

Fine mapping

Fine mapping was performed by evaluating the genotype-phenotype relationship for variants nearby the QTL identified from GWA mapping using a vcf containing imputed variants to avoid removing variants with missing genotype information for one or a few strains. Only SNVs were considered in this mapping.



All variants in interval



Divergent regions



Haplotype








Please kindly cite the following publications

  • Lee D, Zdraljevic S, Stevens L, Wang Y, Tanny RE, Crombie TA, Cook DE, Webster AK, Chirakar R, Baugh LR, Sterken M, Braendle C, Felix M-A, Rockman MV, and Andersen EC (2020) Balancing selection maintains ancient genetic diversity in C. elegans. Nature Ecology and Evolution, 2021 Apr 5; DOI: 10.1038/s41559-021-01435-x.
  • Zdraljevic S, Fox BW, Strand C, Panda O, Tenjo-Castano FJ, Brady SC, Crombie TA, Doench JG, Schroeder FC, and Andersen EC (2019) Natural variation in arsenic toxicity is explained by differences in branched chain amino acid catabolism eLife, Apr 8;8: e40260.
  • Cook DE, Zdraljevic S, Roberts JP, Andersen EC (2016) CeNDR, the Caenorhabditis elegans Natural Diversity Resource. Nucleic Acids Research, Jan 4; 45(D1):D650-D657.



## R version 3.6.0 (2019-04-26)
## Platform: x86_64-pc-linux-gnu (64-bit)
## Running under: Red Hat Enterprise Linux Server 7.5 (Maipo)
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## Matrix products: default
## BLAS:   /hpc/software/R/3.6.0/lib64/R/lib/libRblas.so
## LAPACK: /hpc/software/R/3.6.0/lib64/R/lib/libRlapack.so
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##  [9] LC_ADDRESS=C               LC_TELEPHONE=C            
## [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       
## 
## attached base packages:
## [1] stats     graphics  grDevices utils     datasets  methods   base     
## 
## other attached packages:
##  [1] cowplot_1.0.0      ggnewscale_0.4.5   genetics_1.3.8.1.2 mvtnorm_1.0-12    
##  [5] MASS_7.3-51.4      gtools_3.8.1       gdata_2.18.0       combinat_0.0-8    
##  [9] ggrepel_0.8.2      knitr_1.28         ggbeeswarm_0.6.0   DT_0.12           
## [13] plotly_4.9.2       forcats_0.5.1      stringr_1.4.0      dplyr_1.0.7       
## [17] purrr_0.3.4        readr_2.0.1        tidyr_1.1.3        tibble_3.1.4      
## [21] ggplot2_3.3.5      tidyverse_1.3.1   
## 
## loaded via a namespace (and not attached):
##  [1] fs_1.3.1           lubridate_1.7.10   RColorBrewer_1.1-2 httr_1.4.2        
##  [5] tools_3.6.0        backports_1.1.5    utf8_1.1.4         R6_2.4.1          
##  [9] vipor_0.4.5        DBI_1.1.0          lazyeval_0.2.2     colorspace_1.4-1  
## [13] withr_2.4.2        tidyselect_1.1.1   compiler_3.6.0     cli_3.0.1         
## [17] rvest_1.0.1        xml2_1.3.2         labeling_0.3       scales_1.1.0      
## [21] digest_0.6.24      rmarkdown_2.1      pkgconfig_2.0.3    htmltools_0.4.0   
## [25] dbplyr_2.1.1       fastmap_1.0.1      htmlwidgets_1.5.1  rlang_0.4.11      
## [29] readxl_1.3.1       rstudioapi_0.13    shiny_1.4.0        generics_0.0.2    
## [33] farver_2.0.3       jsonlite_1.7.2     crosstalk_1.0.0    magrittr_2.0.1    
## [37] Rcpp_1.0.6         munsell_0.5.0      fansi_0.4.1        lifecycle_1.0.0   
## [41] stringi_1.4.6      yaml_2.2.1         grid_3.6.0         promises_1.1.0    
## [45] crayon_1.4.1       haven_2.4.3        hms_1.1.0          pillar_1.6.2      
## [49] reprex_2.0.1       glue_1.4.2         evaluate_0.14      data.table_1.12.8 
## [53] modelr_0.1.8       vctrs_0.3.8        tzdb_0.1.2         httpuv_1.5.2      
## [57] cellranger_1.1.0   gtable_0.3.0       assertthat_0.2.1   xfun_0.12         
## [61] mime_0.9           xtable_1.8-4       broom_0.7.9        later_1.0.0       
## [65] viridisLite_0.3.0  beeswarm_0.2.3     ellipsis_0.3.2